Methods

Geneid is a program to predict genes in anonymous genomic sequences designed
with a hierarchical structure. In the first step, splice sites, start and stop
codons are predicted and scored along the sequence using Position Weight Arrays
(PWAs). Next, exons are built from the sites. Exons are scored as the sum of the
scores of the defining sites, plus the the log-likelihood ratio of a
Markov Model for coding DNA. Finally, from the set of predicted exons, the gene
structure is assembled, maximizing the sum of the scores of the assembled exons.